LAMMPS (4 Nov 2022)
# two monomer nylon example
# reaction produces a condensed water molecule

units real

boundary p p p

atom_style full

kspace_style pppm 1.0e-4

pair_style lj/class2/coul/long 8.5

angle_style class2

bond_style class2

dihedral_style class2

improper_style class2

read_data tiny_nylon.data   extra/bond/per/atom 5    extra/angle/per/atom 15   extra/dihedral/per/atom 15   extra/improper/per/atom 25   extra/special/per/atom 25
Reading data file ...
  orthogonal box = (-25 -25 -25) to (25 25 25)
  1 by 1 by 1 MPI processor grid
  reading atom labelmap ...
  reading bond labelmap ...
  reading angle labelmap ...
  reading dihedral labelmap ...
  reading improper labelmap ...
  reading atoms ...
  44 atoms
  reading velocities ...
  44 velocities
  scanning bonds ...
  9 = max bonds/atom
  scanning angles ...
  21 = max angles/atom
  scanning dihedrals ...
  29 = max dihedrals/atom
  scanning impropers ...
  29 = max impropers/atom
  reading bonds ...
  42 bonds
  reading angles ...
  74 angles
  reading dihedrals ...
  100 dihedrals
  reading impropers ...
  44 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     6 = max # of 1-3 neighbors
    12 = max # of 1-4 neighbors
    41 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.007 seconds

velocity all create 300.0 4928459 dist gaussian

molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
  1 molecules
  0 fragments
  18 atoms with max type 8
  16 bonds with max type 10
  25 angles with max type 28
  23 dihedrals with max type 36
  2 impropers with max type 3
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
  1 molecules
  0 fragments
  18 atoms with max type 9
  17 bonds with max type 13
  31 angles with max type 27
  39 dihedrals with max type 33
  0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
  1 molecules
  0 fragments
  15 atoms with max type 9
  14 bonds with max type 13
  25 angles with max type 27
  30 dihedrals with max type 33
  0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
  1 molecules
  0 fragments
  15 atoms with max type 11
  13 bonds with max type 15
  19 angles with max type 29
  16 dihedrals with max type 32
  2 impropers with max type 13

thermo 50

# dump 1 all xyz 1 test_vis.xyz

fix myrxns all bond/react stabilization yes statted_grp .03   react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map   react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined

fix 1 statted_grp_REACT nvt temp 300 300 100

# optionally, you can customize behavior of reacting atoms,
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1

thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]

# restart 100 restart1 restart2

run 10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012

@Article{Gissinger17,
 author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
 title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
 journal = {Polymer},
 year =    2017,
 volume =  128,
 pages =   {211--217}
}

@Article{Gissinger20,
 author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
 title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
 journal = {Macromolecules},
 year =    2020,
 volume =  53,
 number =  22,
 pages =   {9953--9961}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM initialization ...
  using 12-bit tables for long-range coulomb (../kspace.cpp:342)
  G vector (1/distance) = 0.05345967
  grid = 2 2 2
  stencil order = 5
  estimated absolute RMS force accuracy = 0.040225597
  estimated relative force accuracy = 0.00012113819
  using double precision KISS FFT
  3d grid and FFT values/proc = 343 8
Generated 55 of 55 mixed pair_coeff terms from sixthpower/geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 10.5
  ghost atom cutoff = 10.5
  binsize = 5.25, bins = 10 10 10
  2 neighbor lists, perpetual/occasional/extra = 1 1 0
  (1) pair lj/class2/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
  (2) fix bond/react, occasional, copy from (1)
      attributes: half, newton on
      pair build: copy
      stencil: none
      bin: none
WARNING: Inconsistent image flags (../domain.cpp:819)
Per MPI rank memory allocation (min/avg/max) = 33.78 | 33.78 | 33.78 Mbytes
   Step          Temp          Press         Density      f_myrxns[1]    f_myrxns[2]  
         0   300            346.78165      0.0034851739   0              0            
        50   283.51963     -47.16359       0.0034851739   1              0            
       100   256.04648      21.778898      0.0034851739   1              1            
       150   450.78138     -11.7887        0.0034851739   1              1            
       200   400.15754      49.489858      0.0034851739   1              1            
       250   347.06066      68.952063      0.0034851739   1              1            
       300   291.89228     -1.5986302      0.0034851739   1              1            
       350   290.25995      17.634558      0.0034851739   1              1            
       400   234.89168      26.36452       0.0034851739   1              1            
       450   305.80709     -28.923896      0.0034851739   1              1            
       500   375.19218     -37.024375      0.0034851739   1              1            
       550   321.86944     -4.6961825      0.0034851739   1              1            
       600   307.2639      -31.393161      0.0034851739   1              1            
       650   255.95833      8.4995589      0.0034851739   1              1            
       700   294.54665     -17.06105       0.0034851739   1              1            
       750   273.08231     -10.7175        0.0034851739   1              1            
       800   249.69175      9.9777683      0.0034851739   1              1            
       850   307.71806     -6.9950048      0.0034851739   1              1            
       900   367.39855      9.9874985      0.0034851739   1              1            
       950   327.57334     -4.7029779      0.0034851739   1              1            
      1000   348.85247      15.763492      0.0034851739   1              1            
      1050   328.94435     -35.031279      0.0034851739   1              1            
      1100   283.23971     -16.937443      0.0034851739   1              1            
      1150   266.69676      42.308482      0.0034851739   1              1            
      1200   244.61493     -8.291143       0.0034851739   1              1            
      1250   206.68495      6.6280168      0.0034851739   1              1            
      1300   257.83339     -7.0826267      0.0034851739   1              1            
      1350   358.0875      -7.6024741      0.0034851739   1              1            
      1400   353.66614      18.091914      0.0034851739   1              1            
      1450   302.27969      13.828755      0.0034851739   1              1            
      1500   262.57851      9.256794       0.0034851739   1              1            
      1550   252.39493      1.2438641      0.0034851739   1              1            
      1600   247.18352      10.008173      0.0034851739   1              1            
      1650   290.30112     -2.1829035      0.0034851739   1              1            
      1700   272.78999     -57.305766      0.0034851739   1              1            
      1750   253.35258      24.729795      0.0034851739   1              1            
      1800   278.67831     -0.95016566     0.0034851739   1              1            
      1850   302.04743      16.002867      0.0034851739   1              1            
      1900   330.67188     -22.034206      0.0034851739   1              1            
      1950   342.64206      8.0076017      0.0034851739   1              1            
      2000   348.74388     -12.159887      0.0034851739   1              1            
      2050   300.48093      36.01054       0.0034851739   1              1            
      2100   275.01699      8.7612261      0.0034851739   1              1            
      2150   303.92758      10.317056      0.0034851739   1              1            
      2200   308.89457      33.245018      0.0034851739   1              1            
      2250   265.74177      35.857118      0.0034851739   1              1            
      2300   273.40088      53.001593      0.0034851739   1              1            
      2350   287.74746     -0.14590128     0.0034851739   1              1            
      2400   278.76055     -8.2080851      0.0034851739   1              1            
      2450   331.88978      39.025208      0.0034851739   1              1            
      2500   280.04045     -21.423616      0.0034851739   1              1            
      2550   388.81531     -12.350023      0.0034851739   1              1            
      2600   311.13452     -13.287102      0.0034851739   1              1            
      2650   325.07681      88.710878      0.0034851739   1              1            
      2700   319.08502      14.118057      0.0034851739   1              1            
      2750   261.72066      26.051675      0.0034851739   1              1            
      2800   281.03508     -21.200833      0.0034851739   1              1            
      2850   312.27359      4.3892078      0.0034851739   1              1            
      2900   274.81147     -12.738114      0.0034851739   1              1            
      2950   281.76969      11.198451      0.0034851739   1              1            
      3000   291.83918      48.595884      0.0034851739   1              1            
      3050   297.40189     -24.91102       0.0034851739   1              1            
      3100   341.47331      13.82699       0.0034851739   1              1            
      3150   347.51825     -10.458257      0.0034851739   1              1            
      3200   301.24666      26.550464      0.0034851739   1              1            
      3250   281.3679      -23.02985       0.0034851739   1              1            
      3300   279.8332      -53.222264      0.0034851739   1              1            
      3350   289.41496     -8.793156       0.0034851739   1              1            
      3400   288.5722      -25.441134      0.0034851739   1              1            
      3450   259.59524      77.884773      0.0034851739   1              1            
      3500   296.00389      30.3654        0.0034851739   1              1            
      3550   302.14443     -5.1101538      0.0034851739   1              1            
      3600   288.98098     -12.688781      0.0034851739   1              1            
      3650   333.83238     -33.121195      0.0034851739   1              1            
      3700   347.7556      -24.693995      0.0034851739   1              1            
      3750   354.42689      6.7030374      0.0034851739   1              1            
      3800   341.24011     -18.775449      0.0034851739   1              1            
      3850   320.50998      35.492418      0.0034851739   1              1            
      3900   326.81918     -49.073015      0.0034851739   1              1            
      3950   299.55145     -19.487946      0.0034851739   1              1            
      4000   308.81019      30.579971      0.0034851739   1              1            
      4050   251.83279     -17.500379      0.0034851739   1              1            
      4100   242.0783       21.228088      0.0034851739   1              1            
      4150   265.59921     -3.9446469      0.0034851739   1              1            
      4200   369.32464     -14.626205      0.0034851739   1              1            
      4250   346.22904     -32.749662      0.0034851739   1              1            
      4300   369.43175      11.916047      0.0034851739   1              1            
      4350   321.17007     -9.3009147      0.0034851739   1              1            
      4400   312.41821     -31.360537      0.0034851739   1              1            
      4450   281.59211      40.338618      0.0034851739   1              1            
      4500   289.10806     -4.2135222      0.0034851739   1              1            
      4550   317.55705     -4.3727576      0.0034851739   1              1            
      4600   310.64469     -14.403478      0.0034851739   1              1            
      4650   284.43433      37.416848      0.0034851739   1              1            
      4700   353.88469      7.7633789      0.0034851739   1              1            
      4750   328.48834     -60.780145      0.0034851739   1              1            
      4800   390.23986      4.2691385      0.0034851739   1              1            
      4850   364.06188      40.18245       0.0034851739   1              1            
      4900   304.64696      6.3557092      0.0034851739   1              1            
      4950   309.12139     -16.598924      0.0034851739   1              1            
      5000   311.03552      14.748037      0.0034851739   1              1            
      5050   320.97847     -26.733755      0.0034851739   1              1            
      5100   275.1237      -29.734972      0.0034851739   1              1            
      5150   287.76954     -2.5726321      0.0034851739   1              1            
      5200   267.72493     -6.6677739      0.0034851739   1              1            
      5250   290.63862      29.209807      0.0034851739   1              1            
      5300   276.51052     -19.746615      0.0034851739   1              1            
      5350   255.69196      25.130356      0.0034851739   1              1            
      5400   313.43108     -18.556701      0.0034851739   1              1            
      5450   327.91785     -16.08265       0.0034851739   1              1            
      5500   342.03301      33.271603      0.0034851739   1              1            
      5550   272.96564     -5.0247163      0.0034851739   1              1            
      5600   315.93807     -16.793394      0.0034851739   1              1            
      5650   294.66353      19.720691      0.0034851739   1              1            
      5700   283.4631      -6.5193772      0.0034851739   1              1            
      5750   261.06436      12.755679      0.0034851739   1              1            
      5800   274.15767     -9.6693117      0.0034851739   1              1            
      5850   271.1371       18.441828      0.0034851739   1              1            
      5900   283.39277     -4.6324708      0.0034851739   1              1            
      5950   326.30497      12.106133      0.0034851739   1              1            
      6000   316.91847     -32.864812      0.0034851739   1              1            
      6050   344.86369      21.226768      0.0034851739   1              1            
      6100   295.85211     -7.3603837      0.0034851739   1              1            
      6150   256.72292      4.6010174      0.0034851739   1              1            
      6200   248.33379     -20.795929      0.0034851739   1              1            
      6250   259.4054       63.590928      0.0034851739   1              1            
      6300   264.16648      2.6570242      0.0034851739   1              1            
      6350   243.22677     -18.621317      0.0034851739   1              1            
      6400   269.96092      53.832036      0.0034851739   1              1            
      6450   252.06358     -26.231052      0.0034851739   1              1            
      6500   275.4825       25.577441      0.0034851739   1              1            
      6550   298.27441      11.17373       0.0034851739   1              1            
      6600   297.29358     -21.382334      0.0034851739   1              1            
      6650   334.78542      38.892678      0.0034851739   1              1            
      6700   299.48699     -20.336163      0.0034851739   1              1            
      6750   315.01936      21.000444      0.0034851739   1              1            
      6800   244.68344     -6.3625659      0.0034851739   1              1            
      6850   251.56543      27.857872      0.0034851739   1              1            
      6900   280.81518     -12.494398      0.0034851739   1              1            
      6950   273.87437     -34.211085      0.0034851739   1              1            
      7000   274.91068      33.483158      0.0034851739   1              1            
      7050   298.56432     -61.821668      0.0034851739   1              1            
      7100   299.08395      10.365875      0.0034851739   1              1            
      7150   317.38233      29.049831      0.0034851739   1              1            
      7200   317.24932     -27.515026      0.0034851739   1              1            
      7250   305.63931      12.732123      0.0034851739   1              1            
      7300   309.44007     -53.922033      0.0034851739   1              1            
      7350   280.35029      45.495031      0.0034851739   1              1            
      7400   228.60929      1.7072084      0.0034851739   1              1            
      7450   276.206       -19.170327      0.0034851739   1              1            
      7500   257.9851       77.105642      0.0034851739   1              1            
      7550   306.46848     -29.189265      0.0034851739   1              1            
      7600   296.84522     -20.83365       0.0034851739   1              1            
      7650   296.5965      -14.890206      0.0034851739   1              1            
      7700   322.80474      44.883023      0.0034851739   1              1            
      7750   293.7355      -48.487658      0.0034851739   1              1            
      7800   358.41838      13.156339      0.0034851739   1              1            
      7850   293.81457     -19.50566       0.0034851739   1              1            
      7900   309.49618     -28.562417      0.0034851739   1              1            
      7950   285.6339      -22.488886      0.0034851739   1              1            
      8000   262.85312      57.125049      0.0034851739   1              1            
      8050   243.28673     -28.082125      0.0034851739   1              1            
      8100   279.71604      10.011975      0.0034851739   1              1            
      8150   344.77027     -56.89744       0.0034851739   1              1            
      8200   366.36063      21.02453       0.0034851739   1              1            
      8250   347.07209      2.7752885      0.0034851739   1              1            
      8300   337.74753     -10.957676      0.0034851739   1              1            
      8350   300.41188     -22.840776      0.0034851739   1              1            
      8400   282.27447      0.32063982     0.0034851739   1              1            
      8450   285.40722     -3.7167264      0.0034851739   1              1            
      8500   321.32722     -21.308158      0.0034851739   1              1            
      8550   293.65903      15.681219      0.0034851739   1              1            
      8600   293.38929      37.727045      0.0034851739   1              1            
      8650   299.55185     -15.004573      0.0034851739   1              1            
      8700   270.7608       14.615287      0.0034851739   1              1            
      8750   306.46813      67.018302      0.0034851739   1              1            
      8800   308.35025     -91.212286      0.0034851739   1              1            
      8850   349.40419      31.906004      0.0034851739   1              1            
      8900   351.32706     -24.901778      0.0034851739   1              1            
      8950   320.84369      18.380221      0.0034851739   1              1            
      9000   289.2862       9.981138       0.0034851739   1              1            
      9050   270.53883      12.028672      0.0034851739   1              1            
      9100   270.63206     -0.87842772     0.0034851739   1              1            
      9150   274.30671     -4.1228725      0.0034851739   1              1            
      9200   343.78546      20.427647      0.0034851739   1              1            
      9250   348.1019       13.339075      0.0034851739   1              1            
      9300   345.11791     -32.515359      0.0034851739   1              1            
      9350   329.8365       12.644587      0.0034851739   1              1            
      9400   286.41337     -28.79111       0.0034851739   1              1            
      9450   321.92318      32.154255      0.0034851739   1              1            
      9500   302.68527     -42.576022      0.0034851739   1              1            
      9550   335.24034      26.675219      0.0034851739   1              1            
      9600   270.62012      17.230138      0.0034851739   1              1            
      9650   273.71088      35.651219      0.0034851739   1              1            
      9700   286.2141      -26.15835       0.0034851739   1              1            
      9750   262.25352     -4.1954047      0.0034851739   1              1            
      9800   314.29455      23.252049      0.0034851739   1              1            
      9850   273.71272     -29.586039      0.0034851739   1              1            
      9900   300.63743      42.595289      0.0034851739   1              1            
      9950   367.68979     -64.582508      0.0034851739   1              1            
     10000   357.17941      31.607766      0.0034851739   1              1            
Loop time of 1.82433 on 1 procs for 10000 steps with 44 atoms

Performance: 473.599 ns/day, 0.051 hours/ns, 5481.467 timesteps/s, 241.185 katom-step/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.25039    | 0.25039    | 0.25039    |   0.0 | 13.72
Bond    | 1.0461     | 1.0461     | 1.0461     |   0.0 | 57.34
Kspace  | 0.34339    | 0.34339    | 0.34339    |   0.0 | 18.82
Neigh   | 0.0097352  | 0.0097352  | 0.0097352  |   0.0 |  0.53
Comm    | 0.0047764  | 0.0047764  | 0.0047764  |   0.0 |  0.26
Output  | 0.0030537  | 0.0030537  | 0.0030537  |   0.0 |  0.17
Modify  | 0.15534    | 0.15534    | 0.15534    |   0.0 |  8.51
Other   |            | 0.01155    |            |       |  0.63

Nlocal:             44 ave          44 max          44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:             44 ave          44 max          44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:            823 ave         823 max         823 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 823
Ave neighs/atom = 18.704545
Ave special neighs/atom = 9.9090909
Neighbor list builds = 221
Dangerous builds = 0

# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:01
